Known markers expression
Figure 1B : Dotplot showing the expression level of marker genes in each clusters
B-ALL markers: CD34+; RPS14low
B-cell markers: CD19+; CD79A+; CD79B+
Hematogones maturation markers Immature : CD10 (MME) up Mature : CD20 (MS4A1) up
NK-cell markers: NKG7; GNLY; KLRD1; GZMB; KLRC1
Myeloid cells markers LYZ; CD68; LGALS3; CD14; CD33
N.B. some of those markers are only for monocytes/macrophages, therefore the upper part of cluster 2 mostly composed of myeloid progenitors (CMP / MEP / GMP / pro-myelocytes) does not show high expression levels
UMAP visualization of markers expression
DEGs analysis
Differential gene expression analysis:
We search for markers specific to each clusters
The following plots show the expression of each cluster’s top marker based on avg_logFC.
## [1] "PMAIP1 Promotes activation of caspases and apoptosis. Promotes mitochondrial membrane changes and efflux of apoptogenic proteins from the mitochondria. Contributes to p53/TP53-dependent apoptosis after radiation exposure."
## [1] "AC245014.3 is a lincRNA, MUC20 overlapping transcript"
## [1] "PRDX1 : This gene encodes a member of the peroxiredoxin family of antioxidant enzymes, which reduce hydrogen peroxide and alkyl hydroperoxides. The encoded protein may play an antioxidant protective role in cells, and may contribute to the antiviral activity of CD8(+) T-cells. This protein may have a proliferative effect and play a role in cancer development or progression."
## [1] "STMN1 : part of the cell cycle gene list; \nThis gene belongs to the stathmin family of genes. It encodes a ubiquitous cytosolic phosphoprotein proposed to function as an intracellular relay integrating regulatory signals of the cellular environment. The encoded protein is involved in the regulation of the microtubule filament system by destabilizing microtubules. It prevents assembly and promotes disassembly of microtubules."
## [1] "S100A8 : Monocytes marker"
## [1] "S100A9 : Monocytes marker"
## [1] "VPREB1 : this gene belongs to the immunoglobulin superfamily and is expressed selectively at the early stages of B cell development, namely, in proB and early preB cells. This gene encodes the iota polypeptide chain that is associated with the Ig-mu chain to form a molecular complex which is expressed on the surface of pre-B cells. The complex is thought to regulate Ig gene rearrangements in the early steps of B-cell differentiation. Alternative splicing results in multiple transcript variants."
## [1] "DNTT : This gene is a member of the DNA polymerase type-X family and encodes a template-independent DNA polymerase that catalyzes the addition of deoxynucleotides to the 3'-hydroxyl terminus of oligonucleotide primers. In vivo, the encoded protein is expressed in a restricted population of normal and malignant pre-B and pre-T lymphocytes during early differentiation, where it generates antigen receptor diversity by synthesizing non-germ line elements (N-regions) at the junctions of rearranged Ig heavy chain and T cell receptor gene segments."
## [1] "IGKC"
## [1] "IGLL5 : This gene encodes one of the immunoglobulin lambda-like polypeptides. It is located within the immunoglobulin lambda locus but it does not require somatic rearrangement for expression. The first exon of this gene is unrelated to immunoglobulin variable genes; the second and third exons are the immunoglobulin lambda joining 1 and the immunoglobulin lambda constant 1 gene segments."
## [1] "GNLY : The product of this gene is a member of the saposin-like protein (SAPLIP) family and is located in the cytotoxic granules of T cells, which are released upon antigen stimulation. This protein is present in cytotoxic granules of cytotoxic T lymphocytes and natural killer cells, and it has antimicrobial activity against M. tuberculosis and other organisms."
## [1] "NKG7 : natural killer cell group 7 sequence"
